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Here's a few ideas I've been toying with. Most are just fluff, not really in a plot mindset right now.
>After you move into town, your neighbor becomes your mean rival because you moved into their childhood friend's house.
>evil team based on ignorance of the issues they're causing and either don't give a fuck when confronted or do the hokey redemption bullshit. Depends on the tone you're going for.
>I personally prefer the exploration aspect of the series, so while there would be story, ideally you're out there just learning as much as you can about the routes/caves/waterways of the region you set it in, so being a research assistant would be a good twist on the formula. Gyms would essentially be the b plot in this situation.
> If you'd like to forgo the villian team trope, you could play around with alternate conflicts. I'm using invasive species outcompeting native pokemon in my region specifically, but you could have disorganized groups of people who just oppose whatever you're trying to do at that moment, uncatchable boss monsters, natural disasters... Etc.
Not too many and hopefully it's not word spaghetti... feel free to use any of these of course.